BLAST
• Basic Local Alignment Search Tool (1990)
Altschul, Gish, Miller, Myers, & Lipman
Uses short-cuts or “heuristics” to improve
search speed
Like speed-reading, does not examine every
nucleotide of database
However, many more choices (parameters) to
make to adjust search success (over 30!!)
Varieties of BLAST
Program Database Query Typical uses
BLASTN Nucleotide Nucleotide
Mapping oligonucleotides,
cDNAs, and PCR products
to a genome; screening
repetitive elements; cross-
species sequence
exploration; annotating
genomic DNA; clustering
sequencing reads; vector
clipping
BLASTP Protein Protein
Identifying common regions
between proteins;
collecting related proteins
for phylogenetic analyses
BLASTX Protein Nucleotide translated into protein
Finding protein-coding genes in
genomic DNA; determining
if a cDNA corresponds to a
known protein
TBLASTN Nucleotide translated into protein Protein
Identifying transcripts, potentially
from multiple organisms,
similar to a given protein;
mapping a protein to
genomic DNA
TBLASTX Nucleotide translated into protein Nucleotide translated into protein
Cross-species gene prediction at
the genome or transcript
level; searching for genes
missed by traditional
methods or not yet in
protein databases
From: BLAST by Joseph Bedell, Ian Korf, Mark Yandell; O’Rielly 2003
